# vcf file
cat ~/neurogen/rnaseq_PD/results/merged/samplelist.HCILB_SNDA  ~/neurogen/rnaseq_PD/results/merged/samplelist.HC_PY ~/neurogen/rnaseq_PD/results/merged/samplelist.HC_nonNeuron  | awk '{OFS="\t"; split($1,a,"_"); print $1, (a[3]=="SNDA")?"0|0:0:1,0,0":((a[3]~"PY")?"0|1:1:0,1,0":"1|1:2:0,0,1")}' | rowsToCols stdin stdout
bgzip cellType.vcf
tabix -p vcf cellType.vcf.gz

# circRNA raw count
head ~/projects/circRNA/data/Merge_circexplorer_BC106.rawcount.xls -n1 > RIMS2.circRNA.rawcount.txt
grep _73043538 ~/projects/circRNA/data/Merge_circexplorer_BC106.rawcount.xls >> RIMS2.circRNA.rawcount.txt 

# make bam files
# multiple mappers
cat ~/neurogen/rnaseq_PD/results/merged/samplelist.HCILB_SNDA  ~/neurogen/rnaseq_PD/results/merged/samplelist.HC_PY ~/neurogen/rnaseq_PD/results/merged/samplelist.HC_nonNeuron | while read i; do echo $i; samtools view -b -o bam/RIMS1.$i.bam ~/neurogen/rnaseq_PD/run_output/$i/accepted_hits.bam chr6:72550000-73150000; samtools index bam/RIMS1.$i.bam; done
# unique mappers
cat ~/neurogen/rnaseq_PD/results/merged/samplelist.HCILB_SNDA  ~/neurogen/rnaseq_PD/results/merged/samplelist.HC_PY ~/neurogen/rnaseq_PD/results/merged/samplelist.HC_nonNeuron | while read i; do echo $i; samtools view -b -o bam/RIMS1.$i.bam ~/neurogen/rnaseq_PD/run_output/$i/uniq/accepted_hits.bam chr6:72550000-73150000; samtools index bam/RIMS1.$i.bam; done

#make mapping file
>map_file.RIMS1.txt; cat ~/neurogen/rnaseq_PD/results/merged/samplelist.HCILB_SNDA  ~/neurogen/rnaseq_PD/results/merged/samplelist.HC_PY ~/neurogen/rnaseq_PD/results/merged/samplelist.HC_nonNeuron | while read i; do echo $i test_files/bam/RIMS1.$i.bam >> map_file.RIMS1.txt; done

# to getnerate pickle file
python initialize_data.py chr4:90642199 chr6:72550000-73150000 --vcf test_files/cellType.vcf.gz --gtf test_files/RIMS1.gtf --mf test_files/map_file.RIMS1.txt --circ test_files/RIMS1.circRNA.rawcount.txt --output test_files
# to make plot
python plot.py test_files/chr4:90642199@chr6:72550000-73150000.p pickle settings_file

python initialize_data.py chr4:90642199 chr6:72991160-73054014 --vcf test_files/cellType.vcf.gz --gtf test_files/RIMS1.gtf --mf test_files/map_file.RIMS1.txt --circ test_files/RIMS1.circRNA.rawcount.txt --output test_files
python plot.py test_files/chr4:90642199@chr6:72991160-73054014.p pickle settings_file
